Data integration of 104 studies related with microRNA epigenetics revealed that miR-34 gene family is silenced by DNA methylation in the highest number of cancer types

Prognostic impact of miR-34b/c DNA methylation, gene expression, and promoter polymorphism in HPV-negative oral squamous cell carcinomas

Micro RNAs (miRNAs) have a key role in gene expression regulation in cancer. The aim of the current study is to evaluate the prognostic value of miR-34b/c promoter hypermethylation, gene expression, and polymorphism in HPV-negative oral squamous cell carcinomas (OSCC). MiR-34b/c promoter hypermethylation and pre-miR-34b/c polymorphism rs4938723 were evaluated in tumor tissues of 148 patients, and miR-34b expression in 123 HPV-negative OSCC. For risk assessment, the control group was comprised of 175 healthy individuals. MiR-34b/c promoter hypermethylation was determined by methylation-specific PCR. Gene expression, genotyping and HPV screening was assessed by Q-PCR. The data from our hospital cohort indicated that miR-34b/c DNA methylation was associated with nodal status (p = 0.048), and predicted the shorter overall survival of HPV-negative OSCC patients (p = 0.008). Down-regulated miR-34b/c expression was associated with smoking (p = 0.047), alcohol use (p = 0.009), stage (p = 0.025), recurrences (p = 0.000), and a poor survival (p = 0.00029). Median values of miR-34b expression were significantly lower in advanced stages III/IV as opposed to stage I/II, p = 0.006, and in nodal positive vs negative patients (p = 0.045). TCGA data also indicated that tumors with stage I-III expressed significantly higher levels of miR-34b, compared to tumors with stage IV (p = 0.035), Low miR-34b/c expression was associated with poor survival in smokers (p = 0.001) and patients with tongue carcinomas (p = 0.00003), and TCGA analysis confirmed these findings although miR-34b expression and miR-34b/c methylation were not associated with survival outcome in the whole TCGA cohort. A significant negative miR-34b/c expression-methylation correlation was observed in our hospital cohort (p = 0.017) and in TCGA cohort. Pre-miR-34b/c polymorphism was not associated with oral cancer risk. Our findings indicate that miR-34b/c hypermethylation and low miR-34b expression could promote the progression and predict the poor prognosis for HPV-negative OSCC, which suggests miR-34b/c as a promising biomarker and therapeutic target for OSCC in the future.

Epigenetic Regulation of MicroRNA Clusters and Families during Tumor Development

MicroRNAs are small non-coding single-stranded RNA molecules regulating gene expression on a post-transcriptional level based on the seed sequence similarity. They are frequently clustered; thus, they are either simultaneously transcribed into a single polycistronic transcript or they may be transcribed independently. Importantly, microRNA families that contain the same seed region and thus target related signaling proteins, may be localized in one or more clusters, which are in a close relationship. MicroRNAs are involved in basic physiological processes, and their deregulation is associated with the origin of various pathologies, including solid tumors or hematologic malignancies. Recently, the interplay between the expression of microRNA clusters and families and epigenetic machinery was described, indicating aberrant DNA methylation or histone modifications as major mechanisms responsible for microRNA deregulation during cancerogenesis. In this review, the most studied microRNA clusters and families affected by hyper- or hypomethylation as well as by histone modifications are presented with the focus on particular mechanisms. Finally, the diagnostic and prognostic potential of microRNA clusters and families is discussed together with technologies currently used for epigenetic-based cancer therapies.

MicroRNAs in cancer cell death pathways: Apoptosis and necroptosis

To protect tissues and the organism from disease, potentially harmful cells are removed through programmed cell death processes, including apoptosis and necroptosis. These types of cell death are critically controlled by microRNAs (miRNAs). MiRNAs are short RNA molecules that target and inhibit expression of many cellular regulators, including those controlling programmed cell death via the intrinsic (Bcl-2 and Mcl-1), extrinsic (TRAIL and Fas), p53-and endoplasmic reticulum (ER) stress-induced apoptotic pathways, as well as the necroptosis cell death pathway. In this review, we discuss the current knowledge of apoptosis and necroptosis pathways and how these are impaired in cancer cells. We focus on how miRNAs disrupt apoptosis and necroptosis, thereby critically contributing to malignancy. Understanding which and how miRNAs and their targets affect cell death pathways could open up novel therapeutic opportunities for cancer patients. Indeed, restoration of pro-apoptotic tumor suppressor miRNAs (apoptomiRs) or inhibition of oncogenic miRNAs (oncomiRs) represent strategies that are currently being trialed or are already applied as miRNA-based cancer therapies. Therefore, better understanding the cancer type-specific expression of apoptomiRs and oncomiRs and their underlying mechanisms in cell death pathways will not only advance our knowledge, but also continue to provide new opportunities to treat cancer.

The microRNA gene <i>bta-mir-2313</i> in cattle: an atlas of regulatory elements and an association analysis with growth and carcass traits in the Slovenian Simental cattle breed

Abstract. MicroRNAs (miRNA) are a class of non-coding RNAs important in posttranscriptional regulation of target genes. Regulation requires complementarity between the target mRNA and the miRNA region responsible for their recognition and binding, also called the seed region. Previous studies have proven that expression profiles and genetic variations of miRNA genes (miR-SNP; SNP – single nucleotide polymorphism) and their target sites (miR-TS-SNPs) have an impact on phenotypic variation and disease susceptibility in human, animal models, and livestock. MicroRNA-associated polymorphisms therefore represent biomarker potential for phenotypic traits in livestock. Effects of miRNA gene polymorphisms on phenotypic traits have been studied in several animal species but much less in cattle. The aim of the present study was therefore to analyze the genetic variability in the bta-mir-2313 gene and test associations with growth and carcass traits of the Slovenian Simmental cattle breed. Additionally, validated and predicted genomic information related to the miRNA gene bta-mir-2313 has been obtained and presented as an atlas of miRNA regulatory elements. Sanger sequencing has been used for biomarker development and genotyping of 145 animals of Slovenian dual-purpose Simmental cattle. Out of nine known polymorphisms located within pre-miRNA regions, one mature miRNA seed SNP was polymorphic in the Slovenian Simmental cattle breed. An additional three polymorphisms were identified within the flanking pri-miRNA regions. There was no significant effect of polymorphisms on 18 tested fattening and carcass traits; however, validated polymorphisms could now be tested in association with other traits in other cattle populations. The microRNA gene bta-mir-2313 warrants further genetic and functional analyses since it overlaps with a large number of quantitative trait loci (QTL), has over 3100 predicted targets and highly polymorphic mature seed regions, and is located within protein-coding gene GRAMD1B, previously associated with production traits in cattle. Mature miRNA seed SNPs present important genomic loci for functional studies because they could affect the gain/loss of downstream targets and should be systematically studied in cattle.

Methylation profiles of miR34 gene family in Vietnamese patients suffering from breast and lung cancers

The three genes encoding small non‑coding microRNA (miR)34a, MIR34b and MIR34c act as tumor‑suppressor genes. Their aberrant expressions regulated by DNA methylation have been frequently found in various types of cancer. In the present study, the DNA promoter methylation profiles of the MIR34 gene family were analyzed using the methylation specific polymerase chain reaction in order to clarify their association with breast and lung cancer, non‑cancerous or normal adjacent tissues. The methylation frequency of MIR34a was significantly higher in breast cancer (49.37%) compared with normal adjacent tissues (30.38%). The methylation frequency of MIR34b/c was 59.49 and 62.03% in breast cancer and normal adjacent tissues, respectively. MIR34a methylation showed a significant concordance with that of MIR34b/c only in breast cancer tissue. MIR34a methylation was significantly associated with cancer and the invasive ductal carcinoma type of breast cancer (P=0.015 and P=0.02, respectively). Methylation frequency of MIR34a and MIR34b/c was 48.42 and 56.84% in lung cancer, and 47.22 and 51.39% in pulmonary diseases, respectively. No significant association was observed between the methylation status of MIR34a and MIR34b/c, and the clinicopathological features of lung cancer or with those of non‑cancerous pulmonary diseases. Promoter methylation of MIR34a and MIR34b/c occurs frequently and concomitantly in breast and lung cancer, as well as in pulmonary diseases tissues, but not in breast normal tissues adjacent to tumor. These results of the present study emphasize the involvement of MIR34 methylation in human diseases, including cancer. Furthermore, MIR34a methylation may be a promising marker for a subtype of breast cancer.

Classification of miRNA-related sequence variations

miRNA regulome is whole set of regulatory elements that regulate miRNA expression or are under control of miRNAs. Its understanding is vital for comprehension of miRNA functions. Classification of miRNA-related genetic variability is challenging because miRNA interact with different genomic elements and are studied at different omics levels. In the present study, miRNA-associated genetic variability is presented at three levels: miRNA genes and their upstream regulation, miRNA silencing machinery and miRNA targets. Several types of miRNA-associated genetic variations are known, including short and structural polymorphisms and epimutations. Differential expression can also affect miRNA regulome function. Classification of miRNA-associated genetic variability presents a baseline for complementing sequence variant nomenclature, planning of experiments, protocols for multi-omics data integration and development of biomarkers.

MicroRNA Silencing by DNA Methylation in Human Cancer: a Literature Analysis

MicroRNAs (miRNAs) are small non-coding RNAs that post-transcriptionally regulate the expression of target mRNAs. MicroRNA genes themselves are regulated through epigenetic mechanisms, such as histone modifications and/or DNA methylation of CpG islands. Aberrant CpG island methylation patterns are frequently associated with cancer and thus researching DNA methylation of miRNA genes is a topic of increased research interest. Large quantities of available data from various studies are fragmented and incomplete; therefore, integration was performed. Data from 150 articles revealed 180 miRNA genes shown to be regulated via DNA methylation in 36 cancer types. From the total of 2588 known mature miRNA 6.9% (180/2588) miRNAs have been shown to be epigenetically regulated by DNA methylation. 45.5% (82/180) of miRNA genes were shown to be methylated in at least two cancer types among them hsa-miR-34b, hsa-miR-34c and hsa-miR-34a were found to be silenced in 24, 21 and 17 cancer types, respectively. The other 54.4% (98/180) miRNA genes regulated by DNA methylation were found to be specific for a certain type of cancer and therefore represent specific biomarker potential. Because specific miRNAs have diagnostic, prognostic and therapeutic potential, the systematically review of the field offers an overview of the field and facilitates experiment planning, generation of more targeted hypotheses and more efficient biomarker and target development.